Hello,
I have found a bug in CPPTRAJ where aligning a trajectory, saving it, then loading it causes incorrect energies, possibly due to the placement of non-target atoms (that is, atoms in the mask for align). In a minimal example using a small molecule solvated in water, where the trajectory is 2 frames, the following happens:
# script 1
parm example.parm7
trajin example.nc
align !(:WAT)
trajout aligned.nc
energy * etype pme cut 9
go
avg(ENE_00001[total]) # returns -17959.450391 as expected
check
go # no warnings from check
# script 2
parm example.parm7
trajin aligned.nc
energy * etype pme cut 9
go
avg(ENE_00001[total]) # returns 84244.631388
check
go # 10 close contact warnings from check
By varying the energy mask, I have found that the incorrect energy stems from the solvent molecules. In the analysis of a 5 frame long trajectory, the energy after saving and loading was 35591055618150936.000000. This bug happens with V6.4.4 from AmberTools and V6.29.13 from GitHub. Please let me know if there's any more useful information I can provide.
Thank you,
Helmut Carter
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Received on Tue May 27 2025 - 10:00:02 PDT
